The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming ...software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use.
We present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful.
The implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Intrigues: From Being to the Other examines the possibility of writing the other, explores whether an ethical writing that preserves the other as such is possible, and discusses what the implications ...are for an ethically inflected criticism. Emmanuel Levinas and Maurice Blanchot, whose works constitute the most thorough contemporary exploration of the question of the other and of its relation to writing, are the main focus of this study. The book's horizon is ethics in the Levinasian sense: the question of the other, which, on the hither side of language understood as a system of signs and of representation, must be welcomed by language and preserved in its alterity. Martin Heidegger is an unavoidable reference, however. While it is true that for the German philosopher Being is an immanent production, his elucidation of a more essential understanding of Being entails a deconstruction of onto-theology, of the sign and the grammatical and logical determinations of language, all decisive starting points for both Levinas and Blanchot.At stake for both Levinas and Blanchot, then, is how to mark a nondiscursive excess within discourse without erasing or reducing it. How should one read and write the other in the same without reducing the other to the same?Critics in recent years have discussed an ethical moment or turncharacterized by the other's irruption into the order of discourse. The other becomes a true crossroads of disciplines, since it affects several aspects of discourse: the constitution of the subject, the status of knowledge, the nature of representation, and what that representation represses (gender, power). Yet there has been a tendency to graft the other onto paradigms whose main purpose is to reassess questions of identity, fundamentally in terms of representation; the other thus loses some of its most crucial features.Through close readings of texts by Heidegger, Levinas, and Blanchot the book examines how the question of the other engages the very limits of philosophy, rationality, and power.
Abstract
Motivation
Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). ...Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets.
Results
In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified.
Availability and implementation
The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools.
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract
Motivation
Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). ...Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets.
Results
In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified.
Availability and implementation
The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools.
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract MotivationTwo key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). ...Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. ResultsIn this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementationThe implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary informationSupplementary data are available at Bioinformatics online.
To assess the prevalence of candidiasis associated with Linear Gingival Erythema (LGE) in patients with HIV. Material and methods: Patients with HIV who sought care were identified and those with ...linear gingival erythema were included in the study. Initially, a questionnaire divided into two parts was applied, the first session consisting of personal and sociodemographic data and the second session containing questions related to health habits. Then, erythema samples were collected with a collector brush and cultivated in petri dishes containing CHROMagar for 3 days under aerobic conditions at room temperature. Plaque evaluation and colony counts were performed. Results: From a total of 46 patients, thirteen were included in the study. Among the samples, eleven were diagnosed with C. albicans and five were diagnosed with other species of Candida sp. Conclusion: A high prevalence of Candida sp. was observed on patients with lesions of linear gingival erythema and diagnosed with HIV.
...if some strands of ethical criticism—especially in its Anglo-Saxon version that ended up, at best, in a sort of neo-humanism, and at worst in skipping a series of theoretical difficulties that ...reduced or plainly ignored the legacy of literary theory,7 Badiou’s thinking not only subscribes to a radical form of anti-Humanism (he declares himself to be the most faithful follower of both Lacan and Foucault), but also manages to provide a series of answers to difficult issues. ...in the Manifesto for Philosophy, Badiou emphatically contests all affirmations concerning the “end of philosophy” and instead declares that philosophy operates in terms of the concepts of truth, event and subjectivity.12 He specifically rejects the two inflections that the “end of philosophy” has taken in contemporary discourses: the Heideggerian version regarding the exhaustion of metaphysics, as well as the “vulgar” positivist version that sees philosophy superseded by the developments in the natural and human sciences. Newness thus haphazardly deploys truth and the configuration thus put into circulation is inexhaustible: neither reducible to a proper name, nor to a totalizing process able to be placed under a single predicate. ...it is always possible that new works of art can inscribe something unheard of within a particular configuration (art historians employ very general terms to refer to this inscription: impressionism, tonality, etc.). ...any work of art is an inventive inquiry instantiated by an event that engages a beyond-a-previous-given situation by the void that opens within the canonical structures and that belongs to an infinite configuration.
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